Settings: Output files: "/scratch/9142570.1.linga/tophat2/tmp/segment_juncs.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: /scratch/9142570.1.linga/tophat2/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 bmax according to bmaxDivN setting: 5146725 Using parameters --bmax 3860044 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3860044 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 2; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.57336e+06 (target: 3860043) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 3418513 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3418514 Getting block 2 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 2966668 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2966669 Getting block 3 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 3705779 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3705780 Getting block 4 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 1235145 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1235146 Getting block 5 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 3593883 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3593884 Getting block 6 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 1324444 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1324445 Getting block 7 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 3648753 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3648754 Getting block 8 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 693708 (Using difference cover) Sorting block time: 00:00:00 Returning block of 693709 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5078369 fchr[G]: 10291631 fchr[T]: 15389234 fchr[$]: 20586900 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 38854937 bytes to primary EBWT file: /scratch/9142570.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 5146732 bytes to secondary EBWT file: /scratch/9142570.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20586900 bwtLen: 20586901 sz: 5146725 bwtSz: 5146726 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1286682 offsSz: 5146728 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 107224 numLines: 107224 ebwtTotLen: 6862336 ebwtTotSz: 6862336 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:26 Reading reference sizes Time reading reference sizes: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 5146725 Using parameters --bmax 3860044 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3860044 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.57336e+06 (target: 3860043) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 1042032 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1042033 Getting block 2 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 3744543 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3744544 Getting block 3 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 1139961 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1139962 Getting block 4 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 2929425 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2929426 Getting block 5 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 3051935 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3051936 Getting block 6 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 2430191 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2430192 Getting block 7 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 3139366 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3139367 Getting block 8 of 8 Reserving size (3860044) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 3109440 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3109441 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5078369 fchr[G]: 10291631 fchr[T]: 15389234 fchr[$]: 20586900 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 38854937 bytes to primary EBWT file: /scratch/9142570.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 5146732 bytes to secondary EBWT file: /scratch/9142570.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20586900 bwtLen: 20586901 sz: 5146725 bwtSz: 5146726 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1286682 offsSz: 5146728 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 107224 numLines: 107224 ebwtTotLen: 6862336 ebwtTotSz: 6862336 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:22